With Major Motoko Kusanagi absent, Section 9's Batou is tasked to probe a series of brutal killings—apparently carried out by malfunctioning gynoids or sex‑robots. Yet when a defective gynoid leaves him an enigmatic note, he starts to doubt the source of their glitches. Allegations of politically driven homicide and a rogue "ghost" swiftly surface, pulling Batou and his ally Togusa into a treacherous maze of intrigue.
As the probe deepens, distinctions between human and machine blur further, and reality merges with perception. Facing bizarre and perilous adversaries, Batou and Togusa navigate a near‑future landscape brimming with automatons and animated dolls yet utterly bereft of humanity in a city where empathy has vanished.